Atomistry » Magnesium » PDB 5nol-5o5w » 5nx7
Atomistry »
  Magnesium »
    PDB 5nol-5o5w »
      5nx7 »

Magnesium in PDB 5nx7: Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate

Enzymatic activity of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate

All present enzymatic activity of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate:
4.2.3.7;

Protein crystallography data

The structure of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate, PDB code: 5nx7 was solved by V.Karuppiah, D.Leys, N.S.Scrutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.42 / 1.51
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.745, 60.826, 64.258, 92.67, 89.98, 101.77
R / Rfree (%) 14.9 / 17.4

Other elements in 5nx7:

The structure of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate (pdb code 5nx7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate, PDB code: 5nx7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5nx7

Go back to Magnesium Binding Sites List in 5nx7
Magnesium binding site 1 out of 6 in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:18.3
occ:1.00
 O3B A:0FV400 2.0 16.7 0.4
O1A A:0FV400 2.0 20.3 0.4
O3B A:LA6401 2.0 17.4 0.6
O A:HOH533 2.0 21.7 1.0
OE2 A:GLU228 2.1 22.4 1.0
OD1 A:ASN220 2.2 18.0 1.0
O1A A:LA6401 2.2 19.0 0.6
OG A:SER224 2.3 19.7 1.0
CD A:GLU228 3.1 27.2 1.0
PB A:0FV400 3.2 11.6 0.4
CG A:ASN220 3.2 17.8 1.0
PA A:0FV400 3.2 21.5 0.4
PB A:LA6401 3.3 27.7 0.6
CB A:SER224 3.3 18.4 1.0
PA A:LA6401 3.4 17.1 0.6
O3A A:LA6401 3.4 16.0 0.6
O3A A:0FV400 3.4 25.3 0.4
OE1 A:GLU228 3.5 22.9 1.0
ND2 A:ASN220 3.6 18.8 1.0
O2B A:0FV400 3.6 25.0 0.4
O1 A:0FV400 3.8 32.6 0.4
O A:HOH544 3.9 27.5 1.0
O2B A:LA6401 3.9 18.1 0.6
O A:ASN220 4.0 15.3 1.0
O A:HOH572 4.1 22.8 1.0
NH2 A:ARG174 4.2 32.2 1.0
CG A:GLU228 4.3 25.4 1.0
O2A A:LA6401 4.3 16.3 0.6
C1 A:0FV400 4.4 28.8 0.4
C A:ASN220 4.4 14.6 1.0
O2A A:0FV400 4.4 16.2 0.4
OD1 A:ASP221 4.4 19.8 1.0
O1 A:LA6401 4.4 15.5 0.6
O1B A:0FV400 4.5 22.8 0.4
O1B A:LA6401 4.5 19.9 0.6
CB A:ASN220 4.5 16.0 1.0
CA A:SER224 4.7 16.6 1.0
N A:ASP221 4.7 14.8 1.0
CA A:ASP221 4.8 16.1 1.0
C1 A:LA6401 4.8 26.6 0.6
MG A:MG403 4.8 24.9 1.0
O A:SER224 5.0 19.9 1.0
OH A:TYR315 5.0 19.9 1.0

Magnesium binding site 2 out of 6 in 5nx7

Go back to Magnesium Binding Sites List in 5nx7
Magnesium binding site 2 out of 6 in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:24.9
occ:1.00
 O2A A:LA6401 2.0 16.3 0.6
O A:HOH572 2.0 22.8 1.0
O2B A:LA6401 2.1 18.1 0.6
OD2 A:ASP81 2.1 29.9 1.0
O A:HOH535 2.1 27.5 1.0
O A:HOH568 2.2 27.4 1.0
O2B A:0FV400 2.5 25.0 0.4
O3A A:0FV400 2.9 25.3 0.4
PA A:LA6401 3.1 17.1 0.6
O2A A:0FV400 3.1 16.2 0.4
CG A:ASP81 3.1 45.7 1.0
MG A:MG404 3.2 39.0 1.0
PB A:LA6401 3.3 27.7 0.6
PB A:0FV400 3.3 11.6 0.4
O3A A:LA6401 3.3 16.0 0.6
PA A:0FV400 3.4 21.5 0.4
OD1 A:ASP81 3.5 32.8 1.0
O1A A:0FV400 3.8 20.3 0.4
O1A A:LA6401 3.8 19.0 0.6
O A:HOH687 4.0 59.7 1.0
NZ A:LYS227 4.0 28.7 1.0
O3B A:LA6401 4.1 17.4 0.6
NH2 A:ARG314 4.1 24.3 1.0
OE2 A:GLU228 4.2 22.4 1.0
O1B A:0FV400 4.3 22.8 0.4
O A:HOH560 4.4 34.8 1.0
O3B A:0FV400 4.4 16.7 0.4
O1B A:LA6401 4.4 19.9 0.6
O A:HOH627 4.4 35.9 1.0
O1 A:LA6401 4.5 15.5 0.6
CB A:ASP81 4.5 29.4 1.0
O A:HOH501 4.5 32.3 1.0
O A:HOH544 4.5 27.5 1.0
OD2 A:ASP85 4.6 44.5 1.0
OD1 A:ASP82 4.7 33.3 1.0
O A:HOH502 4.8 29.4 1.0
MG A:MG402 4.8 18.3 1.0
OD1 A:ASP85 4.9 54.7 1.0
O1 A:0FV400 4.9 32.6 0.4
O A:HOH704 4.9 25.8 1.0

Magnesium binding site 3 out of 6 in 5nx7

Go back to Magnesium Binding Sites List in 5nx7
Magnesium binding site 3 out of 6 in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:39.0
occ:1.00
 O A:HOH560 2.1 34.8 1.0
O A:HOH568 2.1 27.4 1.0
O A:HOH502 2.1 29.4 1.0
OD1 A:ASP81 2.2 32.8 1.0
O2A A:LA6401 2.2 16.3 0.6
O A:HOH504 2.2 50.5 1.0
O2A A:0FV400 2.2 16.2 0.4
CG A:ASP81 3.1 45.7 1.0
MG A:MG403 3.2 24.9 1.0
OD2 A:ASP81 3.3 29.9 1.0
PA A:LA6401 3.4 17.1 0.6
PA A:0FV400 3.7 21.5 0.4
O1 A:LA6401 3.7 15.5 0.6
O A:HOH546 3.8 38.2 1.0
O A:HOH627 3.8 35.9 1.0
OE2 A:GLU155 4.1 32.6 0.6
O A:HOH544 4.2 27.5 1.0
O A:HOH501 4.2 32.3 1.0
O3A A:0FV400 4.3 25.3 0.4
O1A A:LA6401 4.3 19.0 0.6
OE1 A:GLU155 4.4 38.0 0.6
O A:HOH572 4.4 22.8 1.0
CB A:ASP81 4.5 29.4 1.0
O1A A:0FV400 4.5 20.3 0.4
CZ A:PHE77 4.5 23.3 1.0
O3A A:LA6401 4.6 16.0 0.6
CD A:GLU155 4.7 48.2 0.6
O1 A:0FV400 4.7 32.6 0.4
NH1 A:ARG174 4.7 70.9 1.0
CE1 A:PHE77 4.8 24.9 1.0
O A:HOH535 4.9 27.5 1.0
O2B A:LA6401 4.9 18.1 0.6
C1 A:LA6401 4.9 26.6 0.6

Magnesium binding site 4 out of 6 in 5nx7

Go back to Magnesium Binding Sites List in 5nx7
Magnesium binding site 4 out of 6 in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:17.4
occ:1.00
 O2A B:0FV400 1.9 13.3 0.4
O1B B:LA6401 1.9 15.6 0.6
OE2 B:GLU228 2.1 21.4 1.0
O1B B:0FV400 2.1 17.8 0.4
O B:HOH520 2.1 19.8 1.0
OD1 B:ASN220 2.1 17.0 1.0
O2A B:LA6401 2.3 18.0 0.6
OG B:SER224 2.3 18.9 1.0
CD B:GLU228 3.1 22.9 1.0
CG B:ASN220 3.1 15.1 1.0
PB B:LA6401 3.2 12.0 0.6
PA B:0FV400 3.2 15.7 0.4
CB B:SER224 3.3 18.3 1.0
O3A B:LA6401 3.4 15.3 0.6
PB B:0FV400 3.4 36.5 0.4
PA B:LA6401 3.4 19.7 0.6
OE1 B:GLU228 3.5 21.1 1.0
ND2 B:ASN220 3.5 18.8 1.0
O3A B:0FV400 3.6 21.5 0.4
O3B B:LA6401 3.9 19.4 0.6
O3B B:0FV400 3.9 22.9 0.4
O B:HOH543 3.9 26.4 1.0
O1 B:0FV400 4.0 31.8 0.4
O B:ASN220 4.0 15.5 1.0
NH2 B:ARG174 4.1 27.7 1.0
O B:HOH619 4.2 23.6 1.0
C1 B:0FV400 4.3 26.9 0.4
O1A B:LA6401 4.3 17.0 0.6
CG B:GLU228 4.3 23.1 1.0
O1A B:0FV400 4.3 21.0 0.4
OD1 B:ASP221 4.4 18.6 1.0
C B:ASN220 4.4 16.2 1.0
O1 B:LA6401 4.4 16.1 0.6
O2B B:LA6401 4.4 23.7 0.6
CB B:ASN220 4.5 15.1 1.0
O2B B:0FV400 4.6 16.0 0.4
CA B:SER224 4.7 17.5 1.0
C1 B:LA6401 4.7 31.9 0.6
N B:ASP221 4.7 14.8 1.0
CA B:ASP221 4.7 14.7 1.0
MG B:MG403 4.9 22.0 1.0
O B:SER224 5.0 20.3 1.0
OH B:TYR315 5.0 18.7 1.0

Magnesium binding site 5 out of 6 in 5nx7

Go back to Magnesium Binding Sites List in 5nx7
Magnesium binding site 5 out of 6 in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:22.0
occ:1.00
 O B:HOH531 2.0 27.9 1.0
O1A B:LA6401 2.0 17.0 0.6
O B:HOH619 2.0 23.6 1.0
O3B B:LA6401 2.1 19.4 0.6
OD2 B:ASP81 2.1 26.1 1.0
O B:HOH536 2.1 26.7 1.0
O3B B:0FV400 2.5 22.9 0.4
O3A B:0FV400 2.9 21.5 0.4
O1A B:0FV400 3.0 21.0 0.4
CG B:ASP81 3.1 37.5 1.0
PA B:LA6401 3.2 19.7 0.6
MG B:MG404 3.2 30.9 1.0
PB B:0FV400 3.3 36.5 0.4
PA B:0FV400 3.4 15.7 0.4
PB B:LA6401 3.4 12.0 0.6
OD1 B:ASP81 3.4 30.2 1.0
O3A B:LA6401 3.4 15.3 0.6
O2A B:LA6401 3.8 18.0 0.6
NZ B:LYS227 3.9 26.1 1.0
O2A B:0FV400 3.9 13.3 0.4
O B:HOH505 4.1 59.4 1.0
NH2 B:ARG314 4.2 22.9 1.0
O1B B:LA6401 4.2 15.6 0.6
O1B B:0FV400 4.2 17.8 0.4
OE2 B:GLU228 4.3 21.4 1.0
O B:HOH511 4.3 36.2 1.0
O2B B:0FV400 4.4 16.0 0.4
OD2 B:ASP85 4.4 57.0 1.0
O B:HOH543 4.4 26.4 1.0
O B:HOH503 4.4 40.1 1.0
CB B:ASP81 4.5 25.2 1.0
O2B B:LA6401 4.5 23.7 0.6
O1 B:LA6401 4.5 16.1 0.6
O B:HOH636 4.5 36.5 1.0
OD1 B:ASP82 4.7 29.7 1.0
OD1 B:ASP85 4.8 59.4 1.0
O B:HOH524 4.8 31.0 1.0
O1 B:0FV400 4.9 31.8 0.4
O B:HOH702 4.9 24.4 1.0
MG B:MG402 4.9 17.4 1.0

Magnesium binding site 6 out of 6 in 5nx7

Go back to Magnesium Binding Sites List in 5nx7
Magnesium binding site 6 out of 6 in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:30.9
occ:1.00
 O B:HOH511 2.1 36.2 1.0
O B:HOH536 2.1 26.7 1.0
OD1 B:ASP81 2.1 30.2 1.0
O1A B:0FV400 2.2 21.0 0.4
O B:HOH524 2.2 31.0 1.0
O1A B:LA6401 2.2 17.0 0.6
O B:HOH504 2.3 37.2 1.0
CG B:ASP81 3.0 37.5 1.0
MG B:MG403 3.2 22.0 1.0
OD2 B:ASP81 3.3 26.1 1.0
PA B:LA6401 3.4 19.7 0.6
PA B:0FV400 3.6 15.7 0.4
O1 B:LA6401 3.7 16.1 0.6
O B:HOH529 3.7 36.3 1.0
O B:HOH636 3.8 36.5 1.0
O B:HOH503 4.1 40.1 1.0
O B:HOH543 4.2 26.4 1.0
O3A B:0FV400 4.2 21.5 0.4
OE2 B:GLU155 4.2 28.7 0.5
O2A B:LA6401 4.3 18.0 0.6
OE1 B:GLU155 4.3 30.1 0.5
O B:HOH619 4.4 23.6 1.0
CB B:ASP81 4.4 25.2 1.0
O1 B:0FV400 4.5 31.8 0.4
CZ B:PHE77 4.5 23.0 1.0
O2A B:0FV400 4.6 13.3 0.4
O3A B:LA6401 4.6 15.3 0.6
CD B:GLU155 4.7 38.1 0.5
O B:HOH531 4.8 27.9 1.0
CE1 B:PHE77 4.8 26.1 1.0
O3B B:LA6401 4.8 19.4 0.6
O B:HOH590 4.9 64.8 1.0
C1 B:LA6401 4.9 31.9 0.6

Reference:

V.Karuppiah, K.E.Ranaghan, N.G.H.Leferink, L.O.Johannissen, M.Shanmugam, A.Ni Cheallaigh, N.J.Bennett, L.J.Kearsey, E.Takano, J.M.Gardiner, M.W.Van Der Kamp, S.Hay, A.J.Mulholland, D.Leys, N.S.Scrutton. Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase. Acs Catal V. 7 6268 2017.
ISSN: ESSN 2155-5435
PubMed: 28966840
DOI: 10.1021/ACSCATAL.7B01924
Page generated: Sun Sep 29 23:41:38 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy